http://lod.bco-dmo.org/id/dataset/840475
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2021-02-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Results of qPCR assessments of the abundance of genes related to nitrification, and measurements of ammonia, urea, nitrite and polyamine concentrations in samples collected on cruise LMG1801 on R/V Laurence M. Gould from January to February 2018
2021-04-08
publication
2021-04-08
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-04-08
publication
https://doi.org/10.26008/1912/bco-dmo.840475.1
James T. Hollibaugh
University of Georgia
principalInvestigator
Brian N. Popp
University of Hawaii at Manoa
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Hollibaugh, J. T., Popp, B. N. (2021) Results of qPCR assessments of the abundance of genes related to nitrification, and measurements of ammonia, urea, nitrite and polyamine concentrations in samples collected on cruise LMG1801 on R/V Laurence M. Gould from January to February 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-04-08 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.840475.1 [access date]
LMG1801 qPCR Dataset Description: Methods and Sampling: <p><strong>Sample Collection</strong>. Samples were collected on the Antarctic continental shelf and slope west of the Antarctic Peninsula within the PAL-LTER sampling domain (<a href="http://pal.lternet.edu/" target="_blank">http://pal.lternet.edu/</a>) during summer (cruise dates 30 Dec 2017 through 12 Feb 2018; sampling dates 5 Jan to 4 Feb 2018) from the ARSV Laurence M Gould (LMG 1801, PAL-LTER cruise 26, DOI:&nbsp;<a href="http://dx.doi.org/10.7284/907858" target="_blank">10.7284/907858</a>). Sampling focused on three or 4 depths at each station chosen to represent the Antarctic Surface Water (ASW, 0 -34 m depth), the Winter Water (WW, the water column temperature minimum, generally between 35 and 174 m) the Circumpolar Deep Water (CDW, 175-1000 m) and slope water (SLOPE, &gt;1000 m, generally ~10 m above the bottom at deep stations on the slope, 2500-3048m). Water samples were collected from Niskin bottles (General Oceanics Inc., Miami, FL, USA) into opaque 2 L HDPE plastic bottles or into aged, acid-washed, sample-rinsed 250 ml polycarbonate bottles (Nalge) completely filled (~270 mL) directly from Niskin bottles as soon as possible after the rosette was secured on deck. Subsequent processing took place in an adjacent laboratory.</p>
<p>Samples for DNA analysis were taken from the 2 L opaque HDPE bottles and were filtered under pressure through 0.22 um pore size Sterivex GVWP filters (EMD Millipore, Billerica, MA, USA) using a peristaltic pump. Residual seawater was expelled from the filter using a syringe filled with air, then ~1.8 ml of lysis buffer (0.75 M sucrose, 40 mM EDTA, 50 mM Tris, pH 8.3) was added to the filter capsule, which was capped and placed in a -20 °C freezer. The frozen samples were aggregated into Ziploc Freezer Bags and transferred to a -80 °C freezer for the remainder of the cruise and for shipping to the laboratory.</p>
<p>Two samples of the Sterivex filtrate (40 mL each into new 50 mL disposable centrifuge tubes, VWR, rinsed 3x with sample) were frozen immediately at -20 °C, then aggregated into Ziploc Freezer Bags and transferred to a -80 ° freezer for the remainder of the cruise and for shipping to the laboratory. These were used for subsequent determination of 1) urea concentration and 2) the natural abundance of&nbsp;<sup>15</sup>N in the nitrite plus nitrate pools (<sup>15</sup>NOₓ hereinafter). An additional sample of the Sterivex filtrate was stored in a polycarbonate bottle at 4 °C for subsequent onboard determination of ammonia concentration by the Holmes et al (1999) o-phthaldialdehyde method and nitrite concentration by the diazo-coupling method (Strickland and Parsons 1972). Technical difficulties encountered during onboard analysis resulted in the loss of ammonium and nitrite data for some samples.</p>
<p>Samples for DNA and chemical analyses were shipped on dry ice from Punta Arenas, Chile to the Hollibaugh laboratory at the University of Georgia. Upon arrival they were stored in a -80 °C freezer until analyzed. Samples for&nbsp;<sup>15</sup>N analysis were shipped on dry ice from Punta Arenas, Chile to the Popp laboratory at the University of Hawaii. Upon arrival they were stored in a -40 °C freezer until analyzed.</p>
<p><strong>Chemical analyses.</strong> Urea content was determined by the diacetyl monoxime method (Rahmatullah and Boyde 1980, Mulvenna and Savidge 1992). Subsamples from samples that were also used to determine oxidation of <sup>15</sup>N supplied as putrescine were sent to Dr. X. Mou's laboratory at Kent State University where they were analyzed to determine polyamine and DFAA content as described previously (Lu et al 2014).</p>
<p><strong>Analysis of gene abundance.</strong> DNA was recovered from Sterivex filters using a lysozyme and proteinase K digestion, followed by purification using a phenol–chloroform extraction following Tolar et al. (2013). Abundances of Archaea and Bacteria genes were determined by quantitative PCR (qPCR) used an iCycler CFX Connect Real-Time PCR Detection System (BioRad) using either SYBR Green I dye (BioRad, Hercules, CA, USA) or TaqMan (Applied Biosystems, Carlsbad, CA, USA) chemistries following published protocols (Kalanetra et al., 2009; Tolar et al., 2013) and the primers and probes listed in the attached Supplemental Files ("<a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840475/Primer_Specs.pdf" target="_blank">Primer_Specs.pdf</a>" or "<a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840475/Primer_Specs.xlsx" target="_blank">Primer_Specs.xlsx</a>"). Reactions were set up in triplicate and analyzed against a range of standards (10¹–10⁷ copies per ul) as described in Tolar et al. (2013). qPCR conditions for Archaea <em>amoA</em>, ammonia-oxidizing Betaproteobacteria <em>amoA</em> and Bacteria 16S rRNA (<em>rrs</em>) genes have been described previously (Kalanetra et al., 2009; Tolar et al., 2013). Thaumarchaeota <em>ureC</em> genes were quantified under the same conditions as <em>amoA</em>, with an annealing temperature of 53 °C (from Alonso-Sáez et al., 2012). Nitrospina <em>rrs</em> genes were quantified as in Mincer et al. (2007). Raw abundance data (copies per ul of DNA extract) were converted to concentrations of genes (copies per liter of seawater) using the volume filtered and the extract volume and assuming 100% extraction efficiency as in Tolar et al. (2013). The percent of total prokaryotes represented by Thaumarchaeota was calculated using <em>rrs</em> gene abundance (Bacteria plus Thaumarchaeota) determined by qPCR and corrected using an average of 1.8 Bacteria <em>rrs</em> genes per genome (Biers et al., 2009) and 1.0 Thaumarchaeota <em>rrs</em> gene per genome, as described previously (Kalanetra et al., 2009).&nbsp;Prokaryote abundance determined by qPCR correlated well with total prokaryote counts made with a flow cytometer by Palmer LTER personnel during LMG 18-01 (model II regression: n=78, r² = 0.45, p&lt;&lt;0.0001; slope = 0.65, 95% CL = 0.49 – 0.82; intercept = 0.36, 95% CL = 0.31 - 0.41 * 10⁹ cells L⁻¹).</p>
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: OPP-1643466 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1643466
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: OPP-1643345 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1643345
completed
James T. Hollibaugh
University of Georgia
706-542-7671
Department of Marine Sciences, University of Georgia
Athens
GA
30602
USA
aquadoc@uga.edu
pointOfContact
Brian N. Popp
University of Hawaii at Manoa
808-956-6206
Department of Earth Sciences 1680 East-West Road
Honolulu
HI
96822
USA
popp@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Event_Log_Number
Cast_Start_ISO_DateTime_UTC
Latitude
Longitude
Description
LTER_Grid_Station_Text
Depth
Temperature
Salinity
bact16S
Thaum_16S
WCA_amoA
WCB_amoA
Thaumarchaeota_ureC
AOB_amoA
NOB_16S_rRNA
Ammonium
Urea
Nitrite
Putrescine
Cadaverine
Norspermidine
Spermidine
Spermine
Niskin bottles (General Oceanics Inc., Miami, FL, USA)
iCycler CFX Connect Real-Time PCR Detection System (BioRad)
theme
None, User defined
event
ISO_DateTime_UTC
latitude
longitude
station
depth
water temperature
salinity
genetic material concentration
Ammonium
Urea
Nitrite
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Niskin bottle
qPCR Thermal Cycler
instrument
BCO-DMO Standard Instruments
LMG1801
service
Deployment Activity
Palmer LTER
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: Chemoautotrophy in Antarctic Bacterioplankton Communities Supported by the Oxidation of Urea-derived Nitrogen
https://www.bco-dmo.org/project/775717
Collaborative Research: Chemoautotrophy in Antarctic Bacterioplankton Communities Supported by the Oxidation of Urea-derived Nitrogen
<p><em>NSF Award Abstract:</em><br />
Part 1: The project addresses fundamental questions regarding the role of nitrification (the conversion of ammonium to nitrate by a two-step process involving two different guilds of microorganisms: ammonia- and nitrite-oxidizers) in the Antarctic marine ecosystem. Specifically, the project seeks to evaluate the contribution of primary production supported by the energy in nitrogen compounds to the overall supply of organic carbon to the food web of the Southern Ocean. Previous measurements indicate that nitrification could contribute about 9% to primary production supporting the Antarctic food web on an annual basis, but those measurements did not include the additional production associated with nitrite oxidation. Additionally, the project will aim to determine the significance of the contribution of other sources of nitrogen, (specifically organic nitrogen and urea released by other organisms) to nitrification because these contributions may not be assessed by standard protocols. Such work will aid in better understanding the basis of the energy for the Antarctic marine ecosystems on an annual basis as well as better aid in understanding the energetics of the ecosystem in times and places where primary production based on light energy is limited (i.e. during the polar night or under sea ice cover).</p>
<p>This project will result in training a postdoctoral researcher and provide undergraduate students opportunities to gain hand-on experience with research on microbial geochemistry. The Palmer Long Term Ecological Research (LTER) activities have focused largely on the interaction between ocean climate and the marine food web affecting top predators. Relatively little effort has been devoted to studying processes related to the microbial geochemistry of nitrogen cycling, yet these are a major themes at other LTER sites. This work will contribute substantially to understanding an important aspect of nitrogen cycling and bacterioplankton production in the study area. The team will be working synergistically and be participating fully in the education and outreach efforts of the Palmer LTER, including making highlights of the findings available for posting to their project web site and participating in any special efforts they have in the area of outreach.</p>
<p>Part 2: The proposed work will quantify oxidation rates of 15N supplied as ammonium, urea and nitrite, allowing the estimation of the contribution of urea-derived N and complete nitrification (ammonia to nitrate) to chemoautotrophy and bacterioplankton production in Antarctic coastal waters. The project will compare these estimates to direct measurements of the incorporation of 14C into organic matter in the dark for an independent estimate of chemoautotrophy. The team aims to collect samples spanning the water column: from surface water (~10 m), winter water (50-100 m) and circumpolar deep water (>150 m); on a cruise surveying the continental shelf and slope west of the Antarctic Peninsula in the austral summer of 2018. Other samples will be taken to measure the concentrations of nitrate, nitrite, ammonia and urea, for qPCR analysis of the abundance of relevant microorganisms, and for studies of related processes. The project will rely on collaboration with the existing Palmer LTER to ensure that ancillary data (bacterioplankton abundance and production, chlorophyll, physical and chemical variables) will be available. The synergistic activities of this project along with the LTER activities will provide a unique opportunity to assess chemoautotrophy in context of the overall ecosystem's dynamics- including both primary and secondary production processes.</p>
Oxidation of Urea N
largerWorkCitation
project
eng; USA
oceans
Palmer LTER
-78.2021
-64.032
-69.2562
-64.032
2018-01-05
2018-02-04
Coastal, shelf and slope waters off the West Antarctic Peninsula, PAL-LTER sampling grid, Lawrence M Gould cruise 18-01
0
BCO-DMO catalogue of parameters from Results of qPCR assessments of the abundance of genes related to nitrification, and measurements of ammonia, urea, nitrite and polyamine concentrations in samples collected on cruise LMG1801 on R/V Laurence M. Gould from January to February 2018
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/840495.rdf
Name: Event_Log_Number
Units: unitless
Description: Sequential numbers keyed to the bridge log of activities
http://lod.bco-dmo.org/id/dataset-parameter/840496.rdf
Name: Cast_Start_ISO_DateTime_UTC
Units: unitless
Description: Date and time of CTD cast, sample collection; 24-hour clock; formatted to ISO8601 standard: YYYY-MM-DDThh:mmZ
http://lod.bco-dmo.org/id/dataset-parameter/840497.rdf
Name: Latitude
Units: degrees North
Description: Latitude in decimal degrees
http://lod.bco-dmo.org/id/dataset-parameter/840498.rdf
Name: Longitude
Units: degrees East
Description: Longitude in decimal degrees
http://lod.bco-dmo.org/id/dataset-parameter/840499.rdf
Name: Description
Units: unitless
Description: Station category
http://lod.bco-dmo.org/id/dataset-parameter/840501.rdf
Name: LTER_Grid_Station_Text
Units: unitless
Description: Station location on the PAL-LTER sampling grid (http://pal.lternet.edu)
http://lod.bco-dmo.org/id/dataset-parameter/840502.rdf
Name: Depth
Units: meters (m)
Description: Depth sampled in meters
http://lod.bco-dmo.org/id/dataset-parameter/840503.rdf
Name: Temperature
Units: degrees Celsius
Description: Water temperature from the CTD in Centigrade degrees
http://lod.bco-dmo.org/id/dataset-parameter/840504.rdf
Name: Salinity
Units: PSU
Description: Salinity calculated from water temperature and conductivity from the ship's CTD, practical salinity units
http://lod.bco-dmo.org/id/dataset-parameter/840505.rdf
Name: bact16S
Units: 10^6 copies L-1
Description: Concentration of Bacteria 16S rRNA genes determined by qPCR in units of 106 copies L-1. "nd" = no data. Limit of detection estimated from volume filtered, DNA extract volume, template volume used per reaction and standard curves is 5 * 106 copies L-1, values
http://lod.bco-dmo.org/id/dataset-parameter/840506.rdf
Name: Thaum_16S
Units: 10^3 copies L-1
Description: Concentration of Marine Group 1 Archaea (Thaumarchaeota) 16S rRNA genes determined by qPCR in units of 103 copies L-1. "nd" = no data. Limit of detection estimated from volume filtered, DNA extract volume, template volume used per reaction and standard curves is 2 * 103 copies L-1, values
http://lod.bco-dmo.org/id/dataset-parameter/840507.rdf
Name: WCA_amoA
Units: 10^3 copies L-1
Description: Concentration of ammonia monooxygenase subunit A genes from the Water Column clade A Thaumarchaeota determined by qPCR in units of 103 copies L-1."nd" = no data. Limit of detection estimated from volume filtered, DNA extract volume, template volume used per reaction and standard curves is 1 * 103 copies L-1, values
http://lod.bco-dmo.org/id/dataset-parameter/840508.rdf
Name: WCB_amoA
Units: 10^3 copies L-1
Description: Concentration of ammonia monooxygenase subunit A genes from the Water Column clade B Thaumarchaeota determined by qPCR in units of 103 copies L-1. "nd" = no data. Limit of detection estimated from volume filtered, DNA extract volume, template volume used per reaction and standard curves is 1 * 103 copies L-1, values
http://lod.bco-dmo.org/id/dataset-parameter/840509.rdf
Name: Thaumarchaeota_ureC
Units: 10^3 copies L-1
Description: Concentration of Thaumarchaeota urease subunit C genes determined by qPCR in units of 103 copies L-1. "nd" = no data. Limit of detection estimated from volume filtered, DNA extract volume, template volume used per reaction and standard curves is 8 * 103 copies L-1, values
http://lod.bco-dmo.org/id/dataset-parameter/840510.rdf
Name: AOB_amoA
Units: 10^3 copies L-1
Description: Concentration of ammonia monooxygenase subunit A genes from Beta-proteobacteria determined by qPCR in units of 103 copies L-1. "nd" = no data. Limit of detection estimated from volume filtered, DNA extract volume, template volume used per reaction and standard curves is 8 * 103 copies L-1, values
http://lod.bco-dmo.org/id/dataset-parameter/840511.rdf
Name: NOB_16S_rRNA
Units: 10^3 copies L-1
Description: Concentration of Nitrospina 16S rRNA genes determined by qPCR in units of 103 copies L-1. "nd" = no data. Limit of detection estimated from volume filtered, DNA extract volume, template volume used per reaction and standard curves is 2 * 103 copies L-1, values
http://lod.bco-dmo.org/id/dataset-parameter/840512.rdf
Name: Ammonium
Units: nanomolar (nM)
Description: Concentration of ammonium in 10-9 mol L-1. "nd" = no data. Precision estimated from mean standard deviation of replicate analyses to be 65 nM, values
http://lod.bco-dmo.org/id/dataset-parameter/840513.rdf
Name: Urea
Units: nanomolar (nM)
Description: Concentration of urea in 10-9 mol L-1. "nd" = no data. Precision estimated from mean standard deviation of replicate analyses to be 10 nM, values
http://lod.bco-dmo.org/id/dataset-parameter/840514.rdf
Name: Nitrite
Units: nanomolar (nM)
Description: Concentration of nitrite in 10-9 mol L-1. "nd" = no data. Precision estimated from mean standard deviation of replicate analyses to be 70 nM, values
http://lod.bco-dmo.org/id/dataset-parameter/840515.rdf
Name: Putrescine
Units: nanomolar (nM)
Description: Concentration of putrescine (1,4 butanediamine) in units of 10-9 mol L-1. "nd" = no data. Limit of detection estimated from standard curves to be 0.1 nM, values
http://lod.bco-dmo.org/id/dataset-parameter/840516.rdf
Name: Cadaverine
Units: nanomolar (nM)
Description: Concentration ofcadaverine (1,5 pentanediamine) in 10-9 mol L-1. "nd" = no data. Limit of detection estimated from standard curves to be 0.1 nM, values
http://lod.bco-dmo.org/id/dataset-parameter/840517.rdf
Name: Norspermidine
Units: nanomolar (nM)
Description: Concentration of norspermidine (N,N'-bis(3-aminopropyl)-1,3-propanediamine) in 10-9 mol L-1. "nd" = no data. Limit of detection estimated from standard curves to be 0.1 nM, values
http://lod.bco-dmo.org/id/dataset-parameter/840518.rdf
Name: Spermidine
Units: nanomolar (nM)
Description: Concentration of spermidine (1,5,10 decanetriamine) in units of 10-9 mol L-1. "nd" = no data. Limit of detection estimated from standard curves to be 0.1 nM, values
http://lod.bco-dmo.org/id/dataset-parameter/840519.rdf
Name: Spermine
Units: nanomolar (nM)
Description: Concentration of spermine (N,N'-bis(3-aminopropyl)-1,4 butanediamine) in units of 10-9 mol L-1. "nd" = no data. Limit of detection estimated from standard curves to be 0.1 nM, values
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
14355
https://darchive.mblwhoilibrary.org/bitstream/1912/26925/1/dataset-840475_qpcr__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.840475.1
download
onLine
dataset
<p><strong>Sample Collection</strong>. Samples were collected on the Antarctic continental shelf and slope west of the Antarctic Peninsula within the PAL-LTER sampling domain (<a href="http://pal.lternet.edu/" target="_blank">http://pal.lternet.edu/</a>) during summer (cruise dates 30 Dec 2017 through 12 Feb 2018; sampling dates 5 Jan to 4 Feb 2018) from the ARSV Laurence M Gould (LMG 1801, PAL-LTER cruise 26, DOI:&nbsp;<a href="http://dx.doi.org/10.7284/907858" target="_blank">10.7284/907858</a>). Sampling focused on three or 4 depths at each station chosen to represent the Antarctic Surface Water (ASW, 0 -34 m depth), the Winter Water (WW, the water column temperature minimum, generally between 35 and 174 m) the Circumpolar Deep Water (CDW, 175-1000 m) and slope water (SLOPE, &gt;1000 m, generally ~10 m above the bottom at deep stations on the slope, 2500-3048m). Water samples were collected from Niskin bottles (General Oceanics Inc., Miami, FL, USA) into opaque 2 L HDPE plastic bottles or into aged, acid-washed, sample-rinsed 250 ml polycarbonate bottles (Nalge) completely filled (~270 mL) directly from Niskin bottles as soon as possible after the rosette was secured on deck. Subsequent processing took place in an adjacent laboratory.</p>
<p>Samples for DNA analysis were taken from the 2 L opaque HDPE bottles and were filtered under pressure through 0.22 um pore size Sterivex GVWP filters (EMD Millipore, Billerica, MA, USA) using a peristaltic pump. Residual seawater was expelled from the filter using a syringe filled with air, then ~1.8 ml of lysis buffer (0.75 M sucrose, 40 mM EDTA, 50 mM Tris, pH 8.3) was added to the filter capsule, which was capped and placed in a -20 °C freezer. The frozen samples were aggregated into Ziploc Freezer Bags and transferred to a -80 °C freezer for the remainder of the cruise and for shipping to the laboratory.</p>
<p>Two samples of the Sterivex filtrate (40 mL each into new 50 mL disposable centrifuge tubes, VWR, rinsed 3x with sample) were frozen immediately at -20 °C, then aggregated into Ziploc Freezer Bags and transferred to a -80 ° freezer for the remainder of the cruise and for shipping to the laboratory. These were used for subsequent determination of 1) urea concentration and 2) the natural abundance of&nbsp;<sup>15</sup>N in the nitrite plus nitrate pools (<sup>15</sup>NOₓ hereinafter). An additional sample of the Sterivex filtrate was stored in a polycarbonate bottle at 4 °C for subsequent onboard determination of ammonia concentration by the Holmes et al (1999) o-phthaldialdehyde method and nitrite concentration by the diazo-coupling method (Strickland and Parsons 1972). Technical difficulties encountered during onboard analysis resulted in the loss of ammonium and nitrite data for some samples.</p>
<p>Samples for DNA and chemical analyses were shipped on dry ice from Punta Arenas, Chile to the Hollibaugh laboratory at the University of Georgia. Upon arrival they were stored in a -80 °C freezer until analyzed. Samples for&nbsp;<sup>15</sup>N analysis were shipped on dry ice from Punta Arenas, Chile to the Popp laboratory at the University of Hawaii. Upon arrival they were stored in a -40 °C freezer until analyzed.</p>
<p><strong>Chemical analyses.</strong> Urea content was determined by the diacetyl monoxime method (Rahmatullah and Boyde 1980, Mulvenna and Savidge 1992). Subsamples from samples that were also used to determine oxidation of <sup>15</sup>N supplied as putrescine were sent to Dr. X. Mou's laboratory at Kent State University where they were analyzed to determine polyamine and DFAA content as described previously (Lu et al 2014).</p>
<p><strong>Analysis of gene abundance.</strong> DNA was recovered from Sterivex filters using a lysozyme and proteinase K digestion, followed by purification using a phenol–chloroform extraction following Tolar et al. (2013). Abundances of Archaea and Bacteria genes were determined by quantitative PCR (qPCR) used an iCycler CFX Connect Real-Time PCR Detection System (BioRad) using either SYBR Green I dye (BioRad, Hercules, CA, USA) or TaqMan (Applied Biosystems, Carlsbad, CA, USA) chemistries following published protocols (Kalanetra et al., 2009; Tolar et al., 2013) and the primers and probes listed in the attached Supplemental Files ("<a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840475/Primer_Specs.pdf" target="_blank">Primer_Specs.pdf</a>" or "<a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840475/Primer_Specs.xlsx" target="_blank">Primer_Specs.xlsx</a>"). Reactions were set up in triplicate and analyzed against a range of standards (10¹–10⁷ copies per ul) as described in Tolar et al. (2013). qPCR conditions for Archaea <em>amoA</em>, ammonia-oxidizing Betaproteobacteria <em>amoA</em> and Bacteria 16S rRNA (<em>rrs</em>) genes have been described previously (Kalanetra et al., 2009; Tolar et al., 2013). Thaumarchaeota <em>ureC</em> genes were quantified under the same conditions as <em>amoA</em>, with an annealing temperature of 53 °C (from Alonso-Sáez et al., 2012). Nitrospina <em>rrs</em> genes were quantified as in Mincer et al. (2007). Raw abundance data (copies per ul of DNA extract) were converted to concentrations of genes (copies per liter of seawater) using the volume filtered and the extract volume and assuming 100% extraction efficiency as in Tolar et al. (2013). The percent of total prokaryotes represented by Thaumarchaeota was calculated using <em>rrs</em> gene abundance (Bacteria plus Thaumarchaeota) determined by qPCR and corrected using an average of 1.8 Bacteria <em>rrs</em> genes per genome (Biers et al., 2009) and 1.0 Thaumarchaeota <em>rrs</em> gene per genome, as described previously (Kalanetra et al., 2009).&nbsp;Prokaryote abundance determined by qPCR correlated well with total prokaryote counts made with a flow cytometer by Palmer LTER personnel during LMG 18-01 (model II regression: n=78, r² = 0.45, p&lt;&lt;0.0001; slope = 0.65, 95% CL = 0.49 – 0.82; intercept = 0.36, 95% CL = 0.31 - 0.41 * 10⁹ cells L⁻¹).</p>
Specified by the Principal Investigator(s)
- replaced 'NAN' with 'nd' as missing data identifier;
- renamed fields to comply with BCO-DMO naming conventions;
- corrected dates where month and day were reversed;
- converted cast start date/time field to ISO8601 format;
- 2021-03-17: revised/updated the Methods & Sampling section of the metadata;
- 2021-04-08: replaced data file with copy received on 2021-03-18.
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Niskin bottles (General Oceanics Inc., Miami, FL, USA)
Niskin bottles (General Oceanics Inc., Miami, FL, USA)
PI Supplied Instrument Name: Niskin bottles (General Oceanics Inc., Miami, FL, USA) Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
iCycler CFX Connect Real-Time PCR Detection System (BioRad)
iCycler CFX Connect Real-Time PCR Detection System (BioRad)
PI Supplied Instrument Name: iCycler CFX Connect Real-Time PCR Detection System (BioRad) Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).
Cruise: LMG1801
LMG1801
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel